The hooks in the base were used to hold the tubulators in place. Read about that here: 520 base part function Long story short, you don't need to worry about those.

As for the main baffle above the stoker, you definitely need that. Have you tried contacting whoever you bought the boiler from to make sure it wasn't just an oversight when the truck got loaded? If that doesn't work out call your nearest EFM dealer to get a new or used baffle.